Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014816.1 Kokia drynarioides strain JFW-HI SEQ_129858, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 77863
ACGTcount: A:0.34, C:0.15, G:0.18, T:0.33
Warning! 386 characters in sequence are not A, C, G, or T
Found at i:3366 original size:37 final size:40
Alignment explanation
Indices: 3323--3424 Score: 105
Period size: 37 Copynumber: 2.7 Consensus size: 40
3313 AAAATAATAA
3323 TATTTTAATAGTTTAATATTAAATTTAAT-TT-AA-T-ACT
1 TATTTTAATAGTTTAATATTAAATTTAATATTAAAGTGA-T
*
3360 TATTTTAATAGTATT-TTATT-AATTTAATATTAAAGTGAT
1 TATTTTAATAGT-TTAATATTAAATTTAATATTAAAGTGAT
*
3399 TATCTTAATA--TTAA-ATTAAATTTAAT
1 TATTTTAATAGTTTAATATTAAATTTAAT
3425 GTTTATCTTG
Statistics
Matches: 55, Mismatches: 3, Indels: 14
0.76 0.04 0.19
Matches are distributed among these distances:
36 13 0.24
37 26 0.47
38 4 0.07
39 11 0.20
40 1 0.02
ACGTcount: A:0.41, C:0.02, G:0.04, T:0.53
Consensus pattern (40 bp):
TATTTTAATAGTTTAATATTAAATTTAATATTAAAGTGAT
Found at i:3411 original size:31 final size:29
Alignment explanation
Indices: 3376--3433 Score: 71
Period size: 31 Copynumber: 1.9 Consensus size: 29
3366 AATAGTATTT
*
3376 TATTAATTTAATATTAAAGTGATTATCTTAA
1 TATTAAATTAA-ATTAAA-TGATTATCTTAA
* *
3407 TATTAAATTAAATTTAATGTTTATCTT
1 TATTAAATTAAATTAAATGATTATCTT
3434 GTAGATAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 9 0.38
30 5 0.21
31 10 0.42
ACGTcount: A:0.40, C:0.03, G:0.05, T:0.52
Consensus pattern (29 bp):
TATTAAATTAAATTAAATGATTATCTTAA
Found at i:4137 original size:21 final size:23
Alignment explanation
Indices: 4103--4147 Score: 67
Period size: 21 Copynumber: 2.0 Consensus size: 23
4093 ATCAAGGATT
4103 CCCTTCTGTGGTATCGCGATATC
1 CCCTTCTGTGGTATCGCGATATC
*
4126 CCCTT-TG-GGTATCGTGATATC
1 CCCTTCTGTGGTATCGCGATATC
4147 C
1 C
4148 ACCTCTTAAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 14 0.67
22 2 0.10
23 5 0.24
ACGTcount: A:0.13, C:0.29, G:0.22, T:0.36
Consensus pattern (23 bp):
CCCTTCTGTGGTATCGCGATATC
Found at i:5668 original size:24 final size:24
Alignment explanation
Indices: 5639--5754 Score: 106
Period size: 24 Copynumber: 4.8 Consensus size: 24
5629 CGTTGAAATA
*
5639 CGTAAATGTATACAAGCTGATAAG
1 CGTAAATGTATACAAGCTGACAAG
* * * *
5663 CCTAAATGTGTGCAAGCTGACGAG
1 CGTAAATGTATACAAGCTGACAAG
* * *
5687 CGTAAACGTATATAAGCTGACGAG
1 CGTAAATGTATACAAGCTGACAAG
* * * *
5711 CATAAACGTGTGCAAGCTGACAAG
1 CGTAAATGTATACAAGCTGACAAG
**
5735 CGTAAATGTATTTAAGCTGA
1 CGTAAATGTATACAAGCTGA
5755 TGAGTGTATT
Statistics
Matches: 72, Mismatches: 20, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
24 72 1.00
ACGTcount: A:0.36, C:0.16, G:0.24, T:0.23
Consensus pattern (24 bp):
CGTAAATGTATACAAGCTGACAAG
Found at i:5691 original size:48 final size:48
Alignment explanation
Indices: 5639--5755 Score: 162
Period size: 48 Copynumber: 2.4 Consensus size: 48
5629 CGTTGAAATA
* * * *
5639 CGTAAATGTATACAAGCTGATAAGCCTAAATGTGTGCAAGCTGACGAG
1 CGTAAATGTATATAAGCTGATAAGCATAAACGTGTGCAAGCTGACAAG
* **
5687 CGTAAACGTATATAAGCTGACGAGCATAAACGTGTGCAAGCTGACAAG
1 CGTAAATGTATATAAGCTGATAAGCATAAACGTGTGCAAGCTGACAAG
*
5735 CGTAAATGTATTTAAGCTGAT
1 CGTAAATGTATATAAGCTGAT
5756 GAGTGTATTT
Statistics
Matches: 59, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
48 59 1.00
ACGTcount: A:0.36, C:0.16, G:0.24, T:0.24
Consensus pattern (48 bp):
CGTAAATGTATATAAGCTGATAAGCATAAACGTGTGCAAGCTGACAAG
Found at i:5843 original size:24 final size:24
Alignment explanation
Indices: 5811--5871 Score: 59
Period size: 24 Copynumber: 2.5 Consensus size: 24
5801 CTAACGAGCA
* *
5811 TAAATGTATTTAAGCTGACAAGCG
1 TAAACGTATATAAGCTGACAAGCG
* * *
5835 TAAACGTATATAAGTTGATAAGCT
1 TAAACGTATATAAGCTGACAAGCG
* *
5859 TTAACATATATAA
1 TAAACGTATATAA
5872 AATGTTGAGC
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.43, C:0.10, G:0.15, T:0.33
Consensus pattern (24 bp):
TAAACGTATATAAGCTGACAAGCG
Found at i:12811 original size:24 final size:24
Alignment explanation
Indices: 12623--12808 Score: 214
Period size: 24 Copynumber: 7.8 Consensus size: 24
12613 TAAATGTATA
* *
12623 CAAGCTGATGAGTGTAAACGTGTG
1 CAAGCTGACGAGCGTAAACGTGTG
* *
12647 CAAGCTGACGAGCATAAACATGTG
1 CAAGCTGACGAGCGTAAACGTGTG
* * *
12671 CAAGCTGATGAGTGTAAACTTGTG
1 CAAGCTGACGAGCGTAAACGTGTG
* * *
12695 CAAGCTGATGAGCGTAAACATAG-A
1 CAAGCTGACGAGCGTAAACGT-GTG
12719 CAAG-TAGACGAGCGTAAACGTGTG
1 CAAGCT-GACGAGCGTAAACGTGTG
*
12743 CAAGTTGACGAGCGTAAACGTGTG
1 CAAGCTGACGAGCGTAAACGTGTG
* *
12767 CAAGCTGACGAGCATAAATGTGTG
1 CAAGCTGACGAGCGTAAACGTGTG
*
12791 CAAGCTGACAAGCGTAAA
1 CAAGCTGACGAGCGTAAA
12809 TGTATATAAG
Statistics
Matches: 139, Mismatches: 19, Indels: 8
0.84 0.11 0.05
Matches are distributed among these distances:
23 2 0.01
24 135 0.97
25 2 0.01
ACGTcount: A:0.34, C:0.17, G:0.29, T:0.20
Consensus pattern (24 bp):
CAAGCTGACGAGCGTAAACGTGTG
Found at i:25693 original size:29 final size:29
Alignment explanation
Indices: 25570--25971 Score: 301
Period size: 30 Copynumber: 13.6 Consensus size: 29
25560 AATTTATTTT
* *
25570 AAAATTACATTTTAACCCTTTAACTTTTCT
1 AAAATTACATTTTAACCC-TAAACTTTTCC
25600 AAAA-TATCATTTTAACCCTCAAACTTTTCC
1 AAAATTA-CATTTTAACCCT-AAACTTTTCC
25630 AAAATTACATTTTAACCCTTAAACTTTTCC
1 AAAATTACATTTTAACCC-TAAACTTTTCC
* * *
25660 CAAACTACATTTTGACCCTAAACTTTTCC
1 AAAATTACATTTTAACCCTAAACTTTTCC
* * *
25689 AAAACTACATTTTAACCCTTATCTTTT--
1 AAAATTACATTTTAACCCTAAACTTTTCC
* * *
25716 GAAATTGCATTTTAACACTTAAACTTCTT-C
1 AAAATTACATTTTAAC-CCTAAACTT-TTCC
* * *
25746 AAAATTACATTTAAACCCCAAACTTTTCT
1 AAAATTACATTTTAACCCTAAACTTTTCC
* * * *
25775 AAAATTGCATTTTAACCTCTAATCCTTGCC
1 AAAATTACATTTTAACC-CTAAACTTTTCC
* * * *
25805 AAAATTACATTTTGACTCTTAAACTTCTCT
1 AAAATTACATTTTAAC-CCTAAACTTTTCC
* * *
25835 AAAATCATATTTTAATCCCTAAACCTTTT-G
1 AAAATTACATTTTAA-CCCTAAA-CTTTTCC
* * *
25865 AAAATTACATTTTGACCCCTTAACTTCTCC
1 AAAATTACATTTT-AACCCTAAACTTTTCC
* * * * *
25895 AAAATCACTTTTTAACCCTCAAGTCTTCCC
1 AAAATTACATTTTAACCCTAAACT-TTTCC
* * * * *
25925 AAAAATCACTTTTTAACCCCAAACTTCTCG
1 -AAAATTACATTTTAACCCTAAACTTTTCC
*
25955 AAAATCACATTTTAACC
1 AAAATTACATTTTAACC
25972 TCGTATTCTC
Statistics
Matches: 294, Mismatches: 62, Indels: 33
0.76 0.16 0.08
Matches are distributed among these distances:
27 13 0.04
28 8 0.03
29 89 0.30
30 153 0.52
31 31 0.11
ACGTcount: A:0.35, C:0.25, G:0.02, T:0.38
Consensus pattern (29 bp):
AAAATTACATTTTAACCCTAAACTTTTCC
Found at i:25933 original size:31 final size:29
Alignment explanation
Indices: 25886--25971 Score: 102
Period size: 31 Copynumber: 2.9 Consensus size: 29
25876 TTGACCCCTT
25886 AACTTCTCC-AAAATCACTTTTTAACCCTCA
1 AACTTC-CCAAAAATCACTTTTTAACCC-CA
*
25916 AGTCTTCCCAAAAATCACTTTTTAACCCCA
1 A-ACTTCCCAAAAATCACTTTTTAACCCCA
* * *
25946 AACTTCTCGAAAATCACATTTTAACC
1 AACTTCCCAAAAATCACTTTTTAACC
25972 TCGTATTCTC
Statistics
Matches: 49, Mismatches: 5, Indels: 5
0.83 0.08 0.08
Matches are distributed among these distances:
29 21 0.43
30 6 0.12
31 22 0.45
ACGTcount: A:0.35, C:0.31, G:0.02, T:0.31
Consensus pattern (29 bp):
AACTTCCCAAAAATCACTTTTTAACCCCA
Found at i:31143 original size:11 final size:11
Alignment explanation
Indices: 31119--31189 Score: 53
Period size: 10 Copynumber: 6.8 Consensus size: 11
31109 TTCGATGAAG
* *
31119 AAAAATAAATA
1 AAAAAGAAAGA
31130 AAAAAGAAAGA
1 AAAAAGAAAGA
31141 AAAAAG-AAGA
1 AAAAAGAAAGA
31151 AAAATA-AAA-A
1 AAAA-AGAAAGA
* *
31161 TAAAAGAGAG-
1 AAAAAGAAAGA
*
31171 AAAAA-AAAGT
1 AAAAAGAAAGA
31181 AAAAAGAAA
1 AAAAAGAAA
31190 AGAAGAGGTC
Statistics
Matches: 48, Mismatches: 6, Indels: 12
0.73 0.09 0.18
Matches are distributed among these distances:
9 4 0.08
10 23 0.48
11 21 0.44
ACGTcount: A:0.80, C:0.00, G:0.13, T:0.07
Consensus pattern (11 bp):
AAAAAGAAAGA
Found at i:31151 original size:31 final size:31
Alignment explanation
Indices: 31115--31190 Score: 102
Period size: 31 Copynumber: 2.5 Consensus size: 31
31105 CGGATTCGAT
31115 GAAGAAAAATAAATAA-AAAAGAAAGAAAAAA
1 GAAGAAAAATAAA-AATAAAAGAAAGAAAAAA
*
31146 GAAGAAAAATAAAAATAAAAGAGAGAAAAAA
1 GAAGAAAAATAAAAATAAAAGAAAGAAAAAA
*
31177 -AAGTAAAAAGAAAA
1 GAAG-AAAAATAAAA
31191 GAAGAGGTCG
Statistics
Matches: 41, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
30 5 0.12
31 36 0.88
ACGTcount: A:0.79, C:0.00, G:0.14, T:0.07
Consensus pattern (31 bp):
GAAGAAAAATAAAAATAAAAGAAAGAAAAAA
Found at i:31153 original size:20 final size:19
Alignment explanation
Indices: 31130--31188 Score: 66
Period size: 20 Copynumber: 2.9 Consensus size: 19
31120 AAAATAAATA
31130 AAAAAGAAAGAAAAAAGAAG
1 AAAAA-AAAGAAAAAAGAAG
31150 AAAAATAAA-AATAAAAGAGAG
1 AAAAA-AAAGAA-AAAAGA-AG
*
31171 AAAAAAAAGTAAAAAGAA
1 AAAAAAAAGAAAAAAGAA
31189 AAGAAGAGGT
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
19 3 0.09
20 23 0.68
21 8 0.24
ACGTcount: A:0.80, C:0.00, G:0.15, T:0.05
Consensus pattern (19 bp):
AAAAAAAAGAAAAAAGAAG
Found at i:31153 original size:21 final size:22
Alignment explanation
Indices: 31116--31195 Score: 53
Period size: 21 Copynumber: 3.7 Consensus size: 22
31106 GGATTCGATG
* *
31116 AAGAAAAATA-AATAAAAAAGA
1 AAGAAAAAGAGAAGAAAAAAGA
*
31137 AAGAAAAA-AGAAGAAAAATAAA
1 AAGAAAAAGAGAAGAAAAA-AGA
*
31159 AATAAAAGAGAGAA-AAAAAAGTA
1 AAGAAAA-AGAGAAGAAAAAAG-A
31182 AA-AAGAAA-AGAAGA
1 AAGAA-AAAGAGAAGA
31196 GGTCGAGGTG
Statistics
Matches: 48, Mismatches: 4, Indels: 13
0.74 0.06 0.20
Matches are distributed among these distances:
20 1 0.02
21 19 0.40
22 13 0.27
23 11 0.23
24 4 0.08
ACGTcount: A:0.79, C:0.00, G:0.15, T:0.06
Consensus pattern (22 bp):
AAGAAAAAGAGAAGAAAAAAGA
Found at i:31177 original size:24 final size:25
Alignment explanation
Indices: 31136--31192 Score: 75
Period size: 25 Copynumber: 2.4 Consensus size: 25
31126 AATAAAAAAG
*
31136 AAAGAAAA-A-AGAAGAAAAA-TAA
1 AAAGAAAAGAGAGAAAAAAAAGTAA
*
31158 AAATAAAAGAGAGAAAAAAAAGTAA
1 AAAGAAAAGAGAGAAAAAAAAGTAA
31183 AAAGAAAAGA
1 AAAGAAAAGA
31193 AGAGGTCGAG
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
22 7 0.24
23 1 0.03
24 9 0.31
25 12 0.41
ACGTcount: A:0.79, C:0.00, G:0.16, T:0.05
Consensus pattern (25 bp):
AAAGAAAAGAGAGAAAAAAAAGTAA
Found at i:32252 original size:97 final size:97
Alignment explanation
Indices: 32095--32442 Score: 405
Period size: 97 Copynumber: 3.6 Consensus size: 97
32085 AAATGAGCCA
* * *
32095 TGATACCATGAAGATTTGAAGGGAAAGGTTGAGGCCGCAACGACAAACCCAATACCTTAGAAGAT
1 TGATACCATGAA-ATGTGATGGGAAAGGTTGAGGCCGCAACGACAAACCCGATACCTTAGAAGAT
* * *
32160 GTGATGGGAAGGATTGAGACCGCAATGACGAAT
65 GTGATGGGGAGGATTGAGGCCGCAATGGCGAAT
* * *
32193 CTGATACCATGAAATGTGATGGGAAAGGTTTA-GCCGCAACTG-CAAACTCGGTACCTTAGAAGA
1 -TGATACCATGAAATGTGATGGGAAAGGTTGAGGCCGCAAC-GACAAACCCGATACCTTAGAAGA
* *
32256 TGTGATGGGGAGGATTGAGGTCGTAATGGCGAATT
64 TGTGATGGGGAGGATTGAGGCCGCAATGGCGAA-T
* * * * * * *
32291 TGATTCCATGAAATGTGATGGGGAAGATTGAGGCCACAACGACGAACCCGATATCTTAG-AGATA
1 TGATACCATGAAATGTGATGGGAAAGGTTGAGGCCGCAACGACAAACCCGATACCTTAGAAGATG
*
32355 TGATGGGGAGGATTGAGGCCGCAATGGCAAAT
66 TGATGGGGAGGATTGAGGCCGCAATGGCGAAT
* * * * * *
32387 TCAGTTCCATGAAATGTGATGGGAAAGGTTGAGGCTGCAACGGCGAACCCGGTACC
1 TGA-TACCATGAAATGTGATGGGAAAGGTTGAGGCCGCAACGACAAACCCGATACC
32443 ATGAAGAGTT
Statistics
Matches: 212, Mismatches: 32, Indels: 12
0.83 0.12 0.05
Matches are distributed among these distances:
96 3 0.01
97 159 0.75
98 38 0.18
99 12 0.06
ACGTcount: A:0.32, C:0.16, G:0.31, T:0.21
Consensus pattern (97 bp):
TGATACCATGAAATGTGATGGGAAAGGTTGAGGCCGCAACGACAAACCCGATACCTTAGAAGATG
TGATGGGGAGGATTGAGGCCGCAATGGCGAAT
Found at i:32445 original size:48 final size:47
Alignment explanation
Indices: 32096--32447 Score: 204
Period size: 48 Copynumber: 7.2 Consensus size: 47
32086 AATGAGCCAT
* * * *
32096 GATACCATGAAGATTTGAAGGGAAAGGTTGAGGCCGCAACGACAAACCC
1 GATACCATGAA-ATGTGATGGG-AAGGTTGAGGCCGCAACGGCGAACCC
* * * * * * *
32145 AATACCTTAGAAGATGTGATGGGAAGGATTGAGACCGCAATGACGAATCT
1 GATACCAT-GAA-ATGTGATGGGAAGG-TTGAGGCCGCAACGGCGAACCC
* * * *
32195 GATACCATGAAATGTGATGGGAAAGGTTTA-GCCGCAACTGCAAACTC
1 GATACCATGAAATGTGATGGG-AAGGTTGAGGCCGCAACGGCGAACCC
* * * * * * ***
32242 GGTACCTTAGAAGATGTGATGGGGAGGATTGAGGTCGTAATGGCGAATTT
1 GATACCAT-GAA-ATGTGATGGGAAGG-TTGAGGCCGCAACGGCGAACCC
* * * *
32292 GATTCCATGAAATGTGATGGGGAAGATTGAGGCCACAACGACGAACCC
1 GATACCATGAAATGTGAT-GGGAAGGTTGAGGCCGCAACGGCGAACCC
* * * * * * * **
32340 GATATCTTAGAGATATGATGGGGAGGATTGAGGCCGCAATGGCAAATTC
1 GATACCAT-GAAATGTGATGGGAAGG-TTGAGGCCGCAACGGCGAACCC
* *
32389 -AGTTCCATGAAATGTGATGGGAAAGGTTGAGGCTGCAACGGCGAACCC
1 GA-TACCATGAAATGTGATGGG-AAGGTTGAGGCCGCAACGGCGAACCC
*
32437 GGTACCATGAA
1 GATACCATGAA
32448 GAGTTGAAGG
Statistics
Matches: 220, Mismatches: 70, Indels: 27
0.69 0.22 0.09
Matches are distributed among these distances:
47 15 0.07
48 87 0.40
49 68 0.31
50 50 0.23
ACGTcount: A:0.32, C:0.16, G:0.31, T:0.21
Consensus pattern (47 bp):
GATACCATGAAATGTGATGGGAAGGTTGAGGCCGCAACGGCGAACCC
Found at i:32785 original size:41 final size:38
Alignment explanation
Indices: 32728--32842 Score: 99
Period size: 39 Copynumber: 2.9 Consensus size: 38
32718 AACTGTAGTC
32728 ATTCCAATCT-TATACCCCTAACCAAGAGGGGCAGATTGAAG
1 ATTCCAATCTCT-TACCCC-AACC-A-AGGGGCAGATTGAAG
* * *
32769 ATTCCAATCTCTTACCCCAATCATGGGGCAGATTGTAG
1 ATTCCAATCTCTTACCCCAACCAAGGGGCAGATTGAAG
** * *
32807 -TCATCCAATCTCTTACCCTGATCATGGGGCAGATTG
1 AT--TCCAATCTCTTACCCCAACCAAGGGGCAGATTG
32843 CAATCATCTG
Statistics
Matches: 66, Mismatches: 5, Indels: 8
0.84 0.06 0.10
Matches are distributed among these distances:
37 1 0.02
38 13 0.20
39 32 0.48
40 3 0.05
41 16 0.24
42 1 0.02
ACGTcount: A:0.28, C:0.26, G:0.19, T:0.27
Consensus pattern (38 bp):
ATTCCAATCTCTTACCCCAACCAAGGGGCAGATTGAAG
Found at i:32820 original size:39 final size:38
Alignment explanation
Indices: 32755--32842 Score: 124
Period size: 39 Copynumber: 2.3 Consensus size: 38
32745 CTAACCAAGA
32755 GGGGCAGATTGAAGATTCCAATCTCTTACCCCAATCAT
1 GGGGCAGATTGAAGATTCCAATCTCTTACCCCAATCAT
* **
32793 GGGGCAGATTGTAG-TCATCCAATCTCTTACCCTGATCAT
1 GGGGCAGATTGAAGAT--TCCAATCTCTTACCCCAATCAT
32832 GGGGCAGATTG
1 GGGGCAGATTG
32843 CAATCATCTG
Statistics
Matches: 45, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
37 1 0.02
38 13 0.29
39 31 0.69
ACGTcount: A:0.25, C:0.24, G:0.24, T:0.27
Consensus pattern (38 bp):
GGGGCAGATTGAAGATTCCAATCTCTTACCCCAATCAT
Found at i:33302 original size:210 final size:208
Alignment explanation
Indices: 32853--33399 Score: 743
Period size: 210 Copynumber: 2.6 Consensus size: 208
32843 CAATCATCTG
** * * * *
32853 AAGCAATAAAGTGGTCATCTTCCTAACGAGATGTAGAGAAGTGAACCAAATCCGTCTTCTTGATG
1 AAGCAATAAAGCAGTCATCTTCCTAATGAGATATAGAGAAGTGGACCAAATCCGTCTTCCTGATG
*
32918 AGATATAGAGAAGTGGATTGAAACAATGAGGAGGTCATCTTCCTGATGAGATACAGAGAAGTAGA
66 AGATATAGAGAAGTGGATTGAAACAATGAGGCGGTCATCTTCCTGATGAGATACAGAGAAGTAGA
* * *
32983 ACAATTCCATGAAACGAAGCTCAATACGAATGAGACTTCAAACCCCATCTTCTTGATGAGATACA
131 ACAAATCAATGAAACGAAGCTCAATACGAATGAAACTTCAAACCCCATCTTCTTGATGAGATACA
33048 GAGAAGTGGGTCA
196 GAGAAGTGGGTCA
* * *
33061 AAGCAATAAAGCAATCGTCTTCCTAATGAGATATAAAGAAGTGGACCAAATCCGTCTTCCTGATG
1 AAGCAATAAAGCAGTCATCTTCCTAATGAGATATAGAGAAGTGGACCAAATCCGTCTTCCTGATG
* * ** * * * *
33126 AGATACAAAGAAGCAGATTAAAACAAGTGATGCTGTCATCTTCCTGATGAGATATAGAGAAGTAG
66 AGATATAGAGAAGTGGATTGAAACAA-TGAGGCGGTCATCTTCCTGATGAGATACAGAGAAGTAG
* ** ** * *
33191 ACCAAATCAATGAAGTGAAGCTCAATGTGAGTGAAACTTCAAACCTCCGTCTTCTTGATGAGATA
130 AACAAATCAATGAAACGAAGCTCAATACGAATGAAACTTCAAACC-CCATCTTCTTGATGAGATA
*
33256 CTGAGAAGTGGGTCA
194 CAGAGAAGTGGGTCA
* * * ** *
33271 AAGCAATAAAGCCGTCATCTTCCTGATGAGATACAGAGAAGTGGACCAAATTTGTCTTCCTAATG
1 AAGCAATAAAGCAGTCATCTTCCTAATGAGATATAGAGAAGTGGACCAAATCCGTCTTCCTGATG
* *
33336 AGATATAGAGAAGTGGATTGAAACAATAAGGCGGTCATCTTCCTGATAAGATACAGAGAAGTAG
66 AGATATAGAGAAGTGGATTGAAACAATGAGGCGGTCATCTTCCTGATGAGATACAGAGAAGTAG
33400 GTCAAGATAA
Statistics
Matches: 289, Mismatches: 48, Indels: 3
0.85 0.14 0.01
Matches are distributed among these distances:
208 77 0.27
209 103 0.36
210 109 0.38
ACGTcount: A:0.37, C:0.17, G:0.22, T:0.24
Consensus pattern (208 bp):
AAGCAATAAAGCAGTCATCTTCCTAATGAGATATAGAGAAGTGGACCAAATCCGTCTTCCTGATG
AGATATAGAGAAGTGGATTGAAACAATGAGGCGGTCATCTTCCTGATGAGATACAGAGAAGTAGA
ACAAATCAATGAAACGAAGCTCAATACGAATGAAACTTCAAACCCCATCTTCTTGATGAGATACA
GAGAAGTGGGTCA
Found at i:33310 original size:48 final size:45
Alignment explanation
Indices: 33240--33447 Score: 135
Period size: 48 Copynumber: 4.6 Consensus size: 45
33230 CAAACCTCCG
* *
33240 TCTTCTTGATGAGATACTGAGAAGTGGGTCAAAGCAATAAAGCCGTCA
1 TCTTCCTGATGAGATACAGAGAAGTGGGTC-AA-CAATAAA-CCGTCA
* * **
33288 TCTTCCTGATGAGATACAGAGAAGT-GG---AC--CAAA--TTTG
1 TCTTCCTGATGAGATACAGAGAAGTGGGTCAACAATAAACCGTCA
* * * * * *
33325 TCTTCCTAATGAGATATAGAGAAGTGGATTGAAACAATAAGGCGGTCA
1 TCTTCCTGATGAGATACAGAGAAGTGG-GT-CAACAATAA-ACCGTCA
* * *
33373 TCTTCCTGATAAGATACAGAGAAGTAGGTCAAGATAATAAACCGATCA
1 TCTTCCTGATGAGATACAGAGAAGTGGGTC-A-ACAATAAACCG-TCA
*
33421 TCTTCCTGATGATATACAGAGAAGTGG
1 TCTTCCTGATGAGATACAGAGAAGTGG
33448 ACCAAATTCG
Statistics
Matches: 120, Mismatches: 26, Indels: 28
0.69 0.15 0.16
Matches are distributed among these distances:
37 24 0.20
38 1 0.01
40 3 0.03
42 1 0.01
43 3 0.03
45 2 0.02
47 6 0.05
48 80 0.67
ACGTcount: A:0.36, C:0.15, G:0.24, T:0.25
Consensus pattern (45 bp):
TCTTCCTGATGAGATACAGAGAAGTGGGTCAACAATAAACCGTCA
Found at i:33382 original size:85 final size:85
Alignment explanation
Indices: 33239--33397 Score: 223
Period size: 85 Copynumber: 1.9 Consensus size: 85
33229 TCAAACCTCC
* * *
33239 GTCTTCTTGATGAGATACTGAGAAGTGGGTCAAAGCAATAAAGCCGTCATCTTCCTGATGAGATA
1 GTCTTCCTAATGAGATACTGAGAAGTGGGTCAAAGCAATAAAGCCGTCATCTTCCTGATAAGATA
33304 CAGAGAAGTGGACCAAATTT
66 CAGAGAAGTGGACCAAATTT
* * * *
33324 GTCTTCCTAATGAGATA-TAGAGAAGTGGATTGAAA-CAATAAGGCGGTCATCTTCCTGATAAGA
1 GTCTTCCTAATGAGATACT-GAGAAGTGG-GTCAAAGCAATAAAGCCGTCATCTTCCTGATAAGA
33387 TACAGAGAAGT
64 TACAGAGAAGT
33398 AGGTCAAGAT
Statistics
Matches: 65, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
84 1 0.02
85 60 0.92
86 4 0.06
ACGTcount: A:0.35, C:0.15, G:0.25, T:0.26
Consensus pattern (85 bp):
GTCTTCCTAATGAGATACTGAGAAGTGGGTCAAAGCAATAAAGCCGTCATCTTCCTGATAAGATA
CAGAGAAGTGGACCAAATTT
Found at i:33438 original size:133 final size:133
Alignment explanation
Indices: 33240--33532 Score: 410
Period size: 133 Copynumber: 2.2 Consensus size: 133
33230 CAAACCTCCG
* * *
33240 TCTTCTTGATGAGATACTGAGAAGTGGGTCAAAGCAATAAAGCCGTCATCTTCCTGATGAGATAC
1 TCTTCCTGATGAGATACAGAGAAGTAGGTCAAAGCAATAAAGCCGTCATCTTCCTGATGAGATAC
* * * *
33305 AGAGAAGTGGACCAAATTTGTCTTCCTAATGAGATATAGAGAAGTGGATTGAAACAATAAGGCGG
66 AGAGAAGTGGACCAAATTCGTCTTCCTAATGAGATACAGAGAAGTGGACTGAAACAATAAGGCAG
33370 TCA
131 TCA
* * *
33373 TCTTCCTGATAAGATACAGAGAAGTAGGTC-AAGATAATAAA-CCGATCATCTTCCTGATGATAT
1 TCTTCCTGATGAGATACAGAGAAGTAGGTCAAAG-CAATAAAGCCG-TCATCTTCCTGATGAGAT
* * * * *
33436 ACAGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAGAGAGGTGGGCTGAAATAATGAGGC
64 ACAGAGAAGTGGACCAAATTCGTCTTCCTAATGAGATACAGAGAAGTGGACTGAAACAATAAGGC
33501 AGTCA
129 AGTCA
*
33506 TCTTTCTGATGAGATACAGAGAAGTAG
1 TCTTCCTGATGAGATACAGAGAAGTAG
33533 ACCAAATCGA
Statistics
Matches: 141, Mismatches: 17, Indels: 4
0.87 0.10 0.02
Matches are distributed among these distances:
132 6 0.04
133 135 0.96
ACGTcount: A:0.35, C:0.15, G:0.25, T:0.25
Consensus pattern (133 bp):
TCTTCCTGATGAGATACAGAGAAGTAGGTCAAAGCAATAAAGCCGTCATCTTCCTGATGAGATAC
AGAGAAGTGGACCAAATTCGTCTTCCTAATGAGATACAGAGAAGTGGACTGAAACAATAAGGCAG
TCA
Found at i:33462 original size:85 final size:85
Alignment explanation
Indices: 33373--33539 Score: 212
Period size: 85 Copynumber: 2.0 Consensus size: 85
33363 AAGGCGGTCA
*
33373 TCTTCCTGATAAGATACAGAGAAGTAGG-TCAAGATAATAAACC-GATCATCTTCCTGATGATAT
1 TCTTCCTGATAAGATACAGAGAAGTAGGCTCAA-ATAATAAACCAG-TCATCTTCCTGATGAGAT
*
33436 ACAGAGAAGTGGACCAAATTCG
64 ACAGAGAAGTAGACCAAATTCG
* * * * * ** *
33458 TCTTCCTGATGAGATACAGAGAGGTGGGCTGAAATAATGAGGCAGTCATCTTTCTGATGAGATAC
1 TCTTCCTGATAAGATACAGAGAAGTAGGCTCAAATAATAAACCAGTCATCTTCCTGATGAGATAC
33523 AGAGAAGTAGACCAAAT
66 AGAGAAGTAGACCAAAT
33540 CGATGAAGCG
Statistics
Matches: 70, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
85 66 0.94
86 4 0.06
ACGTcount: A:0.36, C:0.16, G:0.23, T:0.25
Consensus pattern (85 bp):
TCTTCCTGATAAGATACAGAGAAGTAGGCTCAAATAATAAACCAGTCATCTTCCTGATGAGATAC
AGAGAAGTAGACCAAATTCG
Found at i:33588 original size:342 final size:344
Alignment explanation
Indices: 33028--33742 Score: 988
Period size: 342 Copynumber: 2.1 Consensus size: 344
33018 CTTCAAACCC
* * * *
33028 CATCTTCTTGATGAGATACAGAGAAGTGGGTCAAAGCAATAAAGCAATCGTCTTCCTAATGAGAT
1 CATCTTCCTGATGAGATACAGAGAAGTAGGTCAAAGCAATAAACCAATCATCTTCCTAATGAGAT
* * *
33093 ATAAAGAAGTGGACCAAATCCGTCTTCCTGATGAGATACAAAGAAGCAGATTAAAACAAGTGATG
66 ACAAAGAAGTGGACCAAATCCGTCTTCCTGATGAGATACAAAGAAGCAGACTAAAACAAGTGAGG
* * *
33158 CTGTCATCTTCCTGATGAGATATAGAGAAGTAGACCAAATCAATGAAGTGAAGCTCAATGTGAGT
131 CAGTCATCTTCCTGATGAGATACAGAGAAGTAGACCAAATCAATGAAGCGAAGCTCAATGTGAGT
* * * *
33223 GAAACTTCAAACCTCCGTCTTCTTGATGAGATACTGAGAAGTGGGTCAAAGCAATAAAGCCG-TC
196 GAAACTTCAAACCCCCATCTTCTTGATGAGATACTAAGAAGTGGATCAAAGCAATAAAG-CGATC
* * * *
33287 ATCTTCCTGATGAGATACAGAGAAGTGGACCAAATTTGTCTTCCTAATGAGATATAGAGAAGTGG
260 ATCTTCCTAATGAGATACAGAGAAGTGGACCAAATTCGTCTTCCTAATGAGATACAGAGAAGCGG
*
33352 ATTGAAACAA-TAAGGCGGT
325 ATTAAAACAAGTAAGGCGGT
* * * * *
33371 CATCTTCCTGATAAGATACAGAGAAGTAGGTC-AAGATAATAAACCGATCATCTTCCTGATGATA
1 CATCTTCCTGATGAGATACAGAGAAGTAGGTCAAAG-CAATAAACCAATCATCTTCCTAATGAGA
* * * * ** * * *
33435 TACAGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAGAGAGGTGGGCTGAAATAA-TGAG
65 TACAAAGAAGTGGACCAAATCCGTCTTCCTGATGAGATACAAAGAAGCAGACTAAAACAAGTGAG
* *
33499 GCAGTCATCTTTCTGATGAGATACAGAGAAGTAGACCAAATCGATGAAGCGAAGCTCAATGTGAG
130 GCAGTCATCTTCCTGATGAGATACAGAGAAGTAGACCAAATCAATGAAGCGAAGCTCAATGTGAG
* *
33564 TGAAACTTCGAACCCCCATCTTCTTGATGAGATACTAAGAAGTGGATCAAAGTAATAAAGCGATC
195 TGAAACTTCAAACCCCCATCTTCTTGATGAGATACTAAGAAGTGGATCAAAGCAATAAAGCGATC
* * **
33629 GTCTTCCTAATGAGATACAGAGAAGTGGACCAAATTCGTCTTTCTGGTGAGATACAGAGAAGCGG
260 ATCTTCCTAATGAGATACAGAGAAGTGGACCAAATTCGTCTTCCTAATGAGATACAGAGAAGCGG
* * *
33694 ATTAAAACAAGTGATGCTGT
325 ATTAAAACAAGTAAGGCGGT
33714 CATCTTCCTGATGAGATACAGAGAAGTAG
1 CATCTTCCTGATGAGATACAGAGAAGTAG
33743 ACCAAATCCA
Statistics
Matches: 324, Mismatches: 45, Indels: 6
0.86 0.12 0.02
Matches are distributed among these distances:
341 2 0.01
342 188 0.58
343 134 0.41
ACGTcount: A:0.36, C:0.17, G:0.23, T:0.24
Consensus pattern (344 bp):
CATCTTCCTGATGAGATACAGAGAAGTAGGTCAAAGCAATAAACCAATCATCTTCCTAATGAGAT
ACAAAGAAGTGGACCAAATCCGTCTTCCTGATGAGATACAAAGAAGCAGACTAAAACAAGTGAGG
CAGTCATCTTCCTGATGAGATACAGAGAAGTAGACCAAATCAATGAAGCGAAGCTCAATGTGAGT
GAAACTTCAAACCCCCATCTTCTTGATGAGATACTAAGAAGTGGATCAAAGCAATAAAGCGATCA
TCTTCCTAATGAGATACAGAGAAGTGGACCAAATTCGTCTTCCTAATGAGATACAGAGAAGCGGA
TTAAAACAAGTAAGGCGGT
Found at i:33775 original size:210 final size:208
Alignment explanation
Indices: 33371--33900 Score: 769
Period size: 210 Copynumber: 2.5 Consensus size: 208
33361 ATAAGGCGGT
* * * * *
33371 CATCTTCCTGATAAGATAC-AGAGAAGTAGGTC-AAGATAATAAACCGATCATCTTCCTGATGAT
1 CATCTTCTTGATGAGATACTA-AGAAGT-GGTCAAAG-TAATAAAGCGATCGTCTTCCTGATGAG
* * * * *
33434 ATACAGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAGAGAGGTGGGCTGAAATAATGAG
63 ATACAGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGGACTAAAACAATGAG
* *
33499 GCAGTCATCTTTCTGATGAGATACAGAGAAGTAGACCAAATCGATGAAGCGAAGCTCAATGTGAG
128 GCAGTCATCTTCCTGATGAGATACAGAGAAGTAGACCAAATCCATGAAGCGAAGCTCAATGTGAG
*
33564 TGAAACTTCGAACCCC
193 TGAAACTTCAAACCCC
*
33580 CATCTTCTTGATGAGATACTAAGAAGTGGATCAAAGTAATAAAGCGATCGTCTTCCTAATGAGAT
1 CATCTTCTTGATGAGATACTAAGAAGTGG-TCAAAGTAATAAAGCGATCGTCTTCCTGATGAGAT
* * * *
33645 ACAGAGAAGTGGACCAAATTCGTCTTTCTGGTGAGATACAGAGAAGCGGATTAAAACAAGTGATG
65 ACAGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGGACTAAAACAA-TGAGG
*
33710 CTGTCATCTTCCTGATGAGATACAGAGAAGTAGACCAAATCCATGAAGCGAAGCTCAATGTGAGT
129 CAGTCATCTTCCTGATGAGATACAGAGAAGTAGACCAAATCCATGAAGCGAAGCTCAATGTGAGT
33775 GAAACTTCAAACCCC
194 GAAACTTCAAACCCC
* * *
33790 CATCTTCTTGATGAGATATTGAGAAGTGGGTCAAAGTAATAAAGCAATCGTCTTCCTGATGAGAT
1 CATCTTCTTGATGAGATACTAAGAAGT-GGTCAAAGTAATAAAGCGATCGTCTTCCTGATGAGAT
*
33855 ACAGAGAAGTGGACCAAATTCGTCTTCCT-ATTGAGATACAAAGAAG
65 ACAGAGAAGTGGACCAAATTCGTCTTCCTGA-TGAGATACAGAGAAG
33901 TAGACCAAAT
Statistics
Matches: 289, Mismatches: 26, Indels: 11
0.89 0.08 0.03
Matches are distributed among these distances:
208 2 0.01
209 101 0.35
210 184 0.64
211 2 0.01
ACGTcount: A:0.35, C:0.18, G:0.23, T:0.24
Consensus pattern (208 bp):
CATCTTCTTGATGAGATACTAAGAAGTGGTCAAAGTAATAAAGCGATCGTCTTCCTGATGAGATA
CAGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGGACTAAAACAATGAGGCA
GTCATCTTCCTGATGAGATACAGAGAAGTAGACCAAATCCATGAAGCGAAGCTCAATGTGAGTGA
AACTTCAAACCCC
Found at i:33878 original size:37 final size:37
Alignment explanation
Indices: 33837--33911 Score: 116
Period size: 37 Copynumber: 2.0 Consensus size: 37
33827 AATAAAGCAA
* *
33837 TCGTCTTCCTGA-TGAGATACAGAGAAGTGGACCAAAT
1 TCGTCTTCCT-ATTGAGATACAAAGAAGTAGACCAAAT
33874 TCGTCTTCCTATTGAGATACAAAGAAGTAGACCAAAT
1 TCGTCTTCCTATTGAGATACAAAGAAGTAGACCAAAT
33911 T
1 T
33912 GATAAAGCGA
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
36 1 0.03
37 34 0.97
ACGTcount: A:0.35, C:0.19, G:0.20, T:0.27
Consensus pattern (37 bp):
TCGTCTTCCTATTGAGATACAAAGAAGTAGACCAAAT
Found at i:33904 original size:161 final size:161
Alignment explanation
Indices: 33716--34065 Score: 558
Period size: 161 Copynumber: 2.2 Consensus size: 161
33706 GATGCTGTCA
*
33716 TCTTCCTGATGAGATACAGAGAAGTAGACCAAATCCATGAAGCGAAGCTCAATGTGAGTGAAACT
1 TCTTCCTGATGAGATACAGAGAAGTAGACCAAATCCATAAAGCGAAGCTCAATGTGAGTGAAACT
* * *
33781 TCAAACCCCCATCTTCTTGATGAGATATTGAGAAGTGGGTCAAAGTAATAAAGCAATCGTCTTCC
66 TCAAACCCCCATCTTCTTGATGAGATACTAAGAAGTAGGTCAAAGTAATAAAGCAATCGTCTTCC
33846 TGATGAGATACAGAGAAGTGGACCAAATTCG
131 TGATGAGATACAGAGAAGTGGACCAAATTCG
* **
33877 TCTTCCT-ATTGAGATACAAAGAAGTAGACCAAATTGATAAAGCGAAGCTCAATGTGAGTGAAAC
1 TCTTCCTGA-TGAGATACAGAGAAGTAGACCAAATCCATAAAGCGAAGCTCAATGTGAGTGAAAC
* * ** *
33941 TTCGAACCCCCATCTTCTTGATGAGATACTAAGAAGTAGGTTAAAGTAATAAAGCGGTTGTCTTC
65 TTCAAACCCCCATCTTCTTGATGAGATACTAAGAAGTAGGTCAAAGTAATAAAGCAATCGTCTTC
*
34006 CTGATGAGATACAGAGAAGTTGACCAAATTCG
130 CTGATGAGATACAGAGAAGTGGACCAAATTCG
*
34038 TCTTCCTGATGAGATATAGAGAAGTAGA
1 TCTTCCTGATGAGATACAGAGAAGTAGA
34066 TTAAAATAAG
Statistics
Matches: 172, Mismatches: 15, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
160 1 0.01
161 170 0.99
162 1 0.01
ACGTcount: A:0.36, C:0.17, G:0.22, T:0.25
Consensus pattern (161 bp):
TCTTCCTGATGAGATACAGAGAAGTAGACCAAATCCATAAAGCGAAGCTCAATGTGAGTGAAACT
TCAAACCCCCATCTTCTTGATGAGATACTAAGAAGTAGGTCAAAGTAATAAAGCAATCGTCTTCC
TGATGAGATACAGAGAAGTGGACCAAATTCG
Found at i:34102 original size:371 final size:370
Alignment explanation
Indices: 33515--34204 Score: 1105
Period size: 371 Copynumber: 1.9 Consensus size: 370
33505 ATCTTTCTGA
* *
33515 TGAGATACAGAGAAGTAGACCAAATCGATGAAGCGAAGCTCAATGTGAGTGAAACTTCGAACCCC
1 TGAGATACAAAGAAGTAGACCAAATCGATAAAGCGAAGCTCAATGTGAGTGAAACTTCGAACCCC
33580 CATCTTCTTGATGAGATACTAAGAAGTGGATCAAAGTAATAAAGCGATCGTCTTCCTAATGAGAT
66 CATCTTCTTGATGAGATACTAAGAAGTGGATCAAAGTAATAAAGCGATCGTCTTCCTAATGAGAT
* * * *
33645 ACAGAGAAGTGGACCAAATTCGTCTTTCTGGTGAGATACAGAGAAGCGGATTAAAACAAGTGATG
131 ACAGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCAGATTAAAACAAGTGATA
* *
33710 CTGTCATCTTCCTGATGAGATACAGAGAAGTAGACCAAATCCATGAAGCGAAGCTCAATGTGAGT
196 CAGTCATCTTCCTGATGAGATACAGAGAAGTAAACCAAATCCATGAAGCGAAGCTCAATGTGAGT
* * *
33775 GAAACTTCAAACCCCCATC-TTCTTGATGAGATATTGAGAAGTGGGTCAAAGTAATAAAGCAATC
261 GAAACTTCAAACCCCCATCTTTC-TG-TGAGATACTAAGAAGTGGGTCAAAGAAATAAAGCAATC
33839 GTCTTCCTGATGAGATACAGAGAAGTGGACCAAATTCGTCTTCCTAT
324 GTCTTCCTGATGAGATACAGAGAAGTGGACCAAATTCGTCTTCCTAT
*
33886 TGAGATACAAAGAAGTAGACCAAATTGATAAAGCGAAGCTCAATGTGAGTGAAACTTCGAACCCC
1 TGAGATACAAAGAAGTAGACCAAATCGATAAAGCGAAGCTCAATGTGAGTGAAACTTCGAACCCC
* * * *
33951 CATCTTCTTGATGAGATACTAAGAAGTAGG-TTAAAGTAATAAAGCGGTTGTCTTCCTGATGAGA
66 CATCTTCTTGATGAGATACTAAGAAGT-GGATCAAAGTAATAAAGCGATCGTCTTCCTAATGAGA
* * * *
34015 TACAGAGAAGTTGACCAAATTCGTCTTCCTGATGAGATATAGAGAAGTAGATTAAAATAAGTGAT
130 TACAGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCAGATTAAAACAAGTGAT
* *
34080 ACAGTCATCTTCTTGATGAGATACAGAGAAGTAAACCAAATCGATGAAGCGAAGCTCAATGTGAG
195 ACAGTCATCTTCCTGATGAGATACAGAGAAGTAAACCAAATCCATGAAGCGAAGCTCAATGTGAG
* * * *
34145 TGAAACTTCGATCCTCTATCTTTCTGTGAGATACTAAGAAGTGGGTCAAAGAAATAAAGC
260 TGAAACTTCAAACCCCCATCTTTCTGTGAGATACTAAGAAGTGGGTCAAAGAAATAAAGC
34205 GATCAAATCC
Statistics
Matches: 291, Mismatches: 26, Indels: 5
0.90 0.08 0.02
Matches are distributed among these distances:
370 31 0.11
371 255 0.88
372 5 0.02
ACGTcount: A:0.36, C:0.17, G:0.22, T:0.25
Consensus pattern (370 bp):
TGAGATACAAAGAAGTAGACCAAATCGATAAAGCGAAGCTCAATGTGAGTGAAACTTCGAACCCC
CATCTTCTTGATGAGATACTAAGAAGTGGATCAAAGTAATAAAGCGATCGTCTTCCTAATGAGAT
ACAGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCAGATTAAAACAAGTGATA
CAGTCATCTTCCTGATGAGATACAGAGAAGTAAACCAAATCCATGAAGCGAAGCTCAATGTGAGT
GAAACTTCAAACCCCCATCTTTCTGTGAGATACTAAGAAGTGGGTCAAAGAAATAAAGCAATCGT
CTTCCTGATGAGATACAGAGAAGTGGACCAAATTCGTCTTCCTAT
Found at i:34396 original size:48 final size:48
Alignment explanation
Indices: 34340--34463 Score: 169
Period size: 48 Copynumber: 2.6 Consensus size: 48
34330 CTTCAAACCC
* * * *
34340 TTATCTTCCTGATGAGATACAGAGAAGTGGGTCGAAGCAATGAAGTGG
1 TTATCTTCCTGATGAGATACAGAGAAGTGGGTCAAAGCAATAAAGCGA
34388 TTATCTTCCTGATGAGATACTA-AGAAGTGGGTCAAAGCAATAAAGCGA
1 TTATCTTCCTGATGAGATAC-AGAGAAGTGGGTCAAAGCAATAAAGCGA
** *
34436 TCGTCTTCCTGATGAGATATAGAGAAGT
1 TTATCTTCCTGATGAGATACAGAGAAGT
34464 TGACCAAATT
Statistics
Matches: 67, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
47 1 0.01
48 65 0.97
49 1 0.01
ACGTcount: A:0.33, C:0.14, G:0.27, T:0.27
Consensus pattern (48 bp):
TTATCTTCCTGATGAGATACAGAGAAGTGGGTCAAAGCAATAAAGCGA
Found at i:34555 original size:86 final size:85
Alignment explanation
Indices: 34390--34558 Score: 223
Period size: 86 Copynumber: 2.0 Consensus size: 85
34380 TGAAGTGGTT
* * *
34390 ATCTTCCTGATGAGATACTAAGAAGTGGGTCAAAGCAATAAAGCGATCGTCTTCCTGATGAGATA
1 ATCTTCCTGATGAGATACTAAGAAGTGGATCAAAACAATAAAGCGATCATCTTCCTGATGAGATA
* *
34455 TAGAGAAGTTGACCAAATTC
66 CAGAGAAGTAGACCAAATTC
* * * * *
34475 ATCTTCTTGATGAGATAC-AGAGAAGTGGATTAAAACAAATGAGGCGGTCATCTTCCTGATGAGA
1 ATCTTCCTGATGAGATACTA-AGAAGTGGATCAAAAC-AATAAAGCGATCATCTTCCTGATGAGA
34539 TACAGAGAAGTAGACCAAAT
64 TACAGAGAAGTAGACCAAAT
34559 CAAATGAAGC
Statistics
Matches: 72, Mismatches: 10, Indels: 3
0.85 0.12 0.04
Matches are distributed among these distances:
84 1 0.01
85 30 0.42
86 41 0.57
ACGTcount: A:0.37, C:0.15, G:0.23, T:0.25
Consensus pattern (85 bp):
ATCTTCCTGATGAGATACTAAGAAGTGGATCAAAACAATAAAGCGATCATCTTCCTGATGAGATA
CAGAGAAGTAGACCAAATTC
Found at i:35640 original size:10 final size:10
Alignment explanation
Indices: 35618--35647 Score: 51
Period size: 10 Copynumber: 2.9 Consensus size: 10
35608 TATTTATTTC
35618 AAAAATAATAA
1 AAAAATAA-AA
35629 AAAAATAAAA
1 AAAAATAAAA
35639 AAAAATAAA
1 AAAAATAAA
35648 TATGATTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 11 0.58
11 8 0.42
ACGTcount: A:0.87, C:0.00, G:0.00, T:0.13
Consensus pattern (10 bp):
AAAAATAAAA
Found at i:36298 original size:30 final size:29
Alignment explanation
Indices: 36245--36670 Score: 275
Period size: 29 Copynumber: 14.5 Consensus size: 29
36235 TTTATTTTAG
* * **
36245 AATTACATCTTAACCCCCTACTTTTCTAA
1 AATTACATTTTGACCCCAAACTTTTCTAA
* *
36274 AATTGCATTTTGGCCACCAAACTTTTCTAA
1 AATTACATTTTGACC-CCAAACTTTTCTAA
* * * *
36304 AATTACATTTTAACCCTTAAACTTCTCAAA
1 AATTACATTTTGACCC-CAAACTTTTCTAA
*
36334 AATTACATTTTGA-CCCAAACTTTTCCAA
1 AATTACATTTTGACCCCAAACTTTTCTAA
* *** *
36362 AATTGCATTTTGACGCTTGAA-TTTTCCAA
1 AATTACATTTTGAC-CCCAAACTTTTCTAA
* * * *
36391 AACTACATTTTGACCCCTAATTTTTCCAA
1 AATTACATTTTGACCCCAAACTTTTCTAA
* *
36420 AATTACATTTTGACCCCAAACTTTTTTGA
1 AATTACATTTTGACCCCAAACTTTTCTAA
* * *
36449 AATTGCATTTTAACCCCTAAACTTCTCTAA
1 AATTACATTTTGACCCC-AAACTTTTCTAA
* *
36479 AATTACATTTTAACCCAAAACTTTTCTAA
1 AATTACATTTTGACCCCAAACTTTTCTAA
* * *
36508 AATTTCATTTTAACCCCTAAACCTTTC-AA
1 AATTACATTTTGACCCC-AAACTTTTCTAA
* * * * *
36537 AATTATATTTTAACCCTTAAAC-TATCCAA
1 AATTACATTTTGACCC-CAAACTTTTCTAA
* * * * * *
36566 TATCACATTTTAATCCCTAAACCTTTCCAA
1 AATTACATTTTGA-CCCCAAACTTTTCTAA
* * * * *
36596 AATTACATTTTGATCTCGAACTTCTCCAA
1 AATTACATTTTGACCCCAAACTTTTCTAA
* * * * *
36625 AATCACGTTTTGATCCTCAAACCTTCCTAA
1 AATTACATTTTGA-CCCCAAACTTTTCTAA
*
36655 AAGTCACATTTTGACC
1 AA-TTACATTTTGACC
36671 TCGTTTTCTC
Statistics
Matches: 316, Mismatches: 68, Indels: 25
0.77 0.17 0.06
Matches are distributed among these distances:
28 28 0.09
29 164 0.52
30 114 0.36
31 10 0.03
ACGTcount: A:0.34, C:0.25, G:0.04, T:0.37
Consensus pattern (29 bp):
AATTACATTTTGACCCCAAACTTTTCTAA
Found at i:36364 original size:58 final size:60
Alignment explanation
Indices: 36264--36606 Score: 326
Period size: 58 Copynumber: 5.8 Consensus size: 60
36254 TTAACCCCCT
* ** *
36264 ACTTTTCTAAAATTGCATTTTGGCCACC-AAACTTTTCTAAAATTACATTTTAACCCTTAA
1 ACTTTTCTAAAATTACATTTTAACC-CCTAAACTTTTCCAAAATTACATTTTAACCCTTAA
* * * * * * *
36324 ACTTCTCAAAAATTACATTTTGA-CCC-AAACTTTTCCAAAATTGCATTTTGACGCTTGA
1 ACTTTTCTAAAATTACATTTTAACCCCTAAACTTTTCCAAAATTACATTTTAACCCTTAA
* * * * * *
36382 A-TTTTCCAAAACTACATTTTGACCCCT-AATTTTTCCAAAATTACATTTTGACCC-CAA
1 ACTTTTCTAAAATTACATTTTAACCCCTAAACTTTTCCAAAATTACATTTTAACCCTTAA
* * * * * *
36439 ACTTTTTTGAAATTGCATTTTAACCCCTAAACTTCTCTAAAATTACATTTTAACCC-AAA
1 ACTTTTCTAAAATTACATTTTAACCCCTAAACTTTTCCAAAATTACATTTTAACCCTTAA
* * *
36498 ACTTTTCTAAAATTTCATTTTAACCCCTAAACCTTT-CAAAATTATATTTTAACCCTTAA
1 ACTTTTCTAAAATTACATTTTAACCCCTAAACTTTTCCAAAATTACATTTTAACCCTTAA
* * * * * *
36557 AC-TATCCAATATCACATTTTAATCCCTAAACCTTTCCAAAATTACATTTT
1 ACTTTTCTAAAATTACATTTTAACCCCTAAACTTTTCCAAAATTACATTTT
36607 GATCTCGAAC
Statistics
Matches: 234, Mismatches: 43, Indels: 13
0.81 0.15 0.04
Matches are distributed among these distances:
57 20 0.09
58 121 0.52
59 74 0.32
60 19 0.08
ACGTcount: A:0.34, C:0.23, G:0.03, T:0.39
Consensus pattern (60 bp):
ACTTTTCTAAAATTACATTTTAACCCCTAAACTTTTCCAAAATTACATTTTAACCCTTAA
Found at i:38815 original size:3 final size:3
Alignment explanation
Indices: 38809--38893 Score: 99
Period size: 3 Copynumber: 30.0 Consensus size: 3
38799 CTAGGGTAGT
* * * *
38809 AGA AGA AGA AG- AGA AAA AGC AGA ATA AG- AGA AGA A-A CGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
38854 AGA AGA A-A AGA AGA AG- AGA AGA AGA AGA AGA AGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
38894 GAAAATGGAA
Statistics
Matches: 69, Mismatches: 8, Indels: 10
0.79 0.09 0.11
Matches are distributed among these distances:
2 9 0.13
3 60 0.87
ACGTcount: A:0.66, C:0.02, G:0.31, T:0.01
Consensus pattern (3 bp):
AGA
Found at i:38841 original size:25 final size:23
Alignment explanation
Indices: 38811--38898 Score: 88
Period size: 25 Copynumber: 3.7 Consensus size: 23
38801 AGGGTAGTAG
*
38811 AAGAAGAAGAGAAAAAGCAGAATA
1 AAGAAGAAGAGAAAAAGAAGAA-A
*
38835 AGAGAAGAA-ACGAAGAAGAAGAAGAA
1 A-AGAAGAAGA-GAAAAAGAAG-A-AA
* *
38861 AAGAAGAAGAGAAGAAGAAGAAG
1 AAGAAGAAGAGAAAAAGAAGAAA
38884 AAGAAGAAGAGAAAA
1 AAGAAGAAGAGAAAA
38899 TGGAAGGAGC
Statistics
Matches: 55, Mismatches: 4, Indels: 11
0.79 0.06 0.16
Matches are distributed among these distances:
23 15 0.27
24 3 0.05
25 32 0.58
26 4 0.07
27 1 0.02
ACGTcount: A:0.67, C:0.02, G:0.30, T:0.01
Consensus pattern (23 bp):
AAGAAGAAGAGAAAAAGAAGAAA
Found at i:38851 original size:28 final size:27
Alignment explanation
Indices: 38809--38896 Score: 99
Period size: 28 Copynumber: 3.1 Consensus size: 27
38799 CTAGGGTAGT
* *
38809 AGAAGAAGAAG-AGAAAAAGCAGAATAAG
1 AGAAG-AGAAGAAGAAGAAGAAGAA-AAG
38837 AGAAGA-AACGAAGAAGAAGAAGAAAAG
1 AGAAGAGAA-GAAGAAGAAGAAGAAAAG
38864 AAGAAGAGAAGAAGAAGAAGAAGAAGAAG
1 -AGAAGAGAAGAAGAAGAAGAAGAA-AAG
38893 AGAA
1 AGAA
38897 AATGGAAGGA
Statistics
Matches: 53, Mismatches: 2, Indels: 10
0.82 0.03 0.15
Matches are distributed among these distances:
26 2 0.04
27 5 0.09
28 41 0.77
29 5 0.09
ACGTcount: A:0.66, C:0.02, G:0.31, T:0.01
Consensus pattern (27 bp):
AGAAGAGAAGAAGAAGAAGAAGAAAAG
Found at i:50491 original size:23 final size:23
Alignment explanation
Indices: 50465--50516 Score: 104
Period size: 23 Copynumber: 2.3 Consensus size: 23
50455 GAAAAAGTAT
50465 GTGTTGGTGAGAATGTATCTGTG
1 GTGTTGGTGAGAATGTATCTGTG
50488 GTGTTGGTGAGAATGTATCTGTG
1 GTGTTGGTGAGAATGTATCTGTG
50511 GTGTTG
1 GTGTTG
50517 TCGCGAAGGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.15, C:0.04, G:0.40, T:0.40
Consensus pattern (23 bp):
GTGTTGGTGAGAATGTATCTGTG
Found at i:53686 original size:5 final size:6
Alignment explanation
Indices: 53672--53706 Score: 52
Period size: 6 Copynumber: 5.7 Consensus size: 6
53662 GGCAACCCAA
*
53672 TTTTAT TTTTAT TTTTAT TTTTAG TTTTAGT TTTT
1 TTTTAT TTTTAT TTTTAT TTTTAT TTTTA-T TTTT
53707 TTTCTTTCAT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
6 22 0.85
7 4 0.15
ACGTcount: A:0.14, C:0.00, G:0.06, T:0.80
Consensus pattern (6 bp):
TTTTAT
Found at i:55030 original size:2 final size:2
Alignment explanation
Indices: 55023--55050 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
55013 GTATATTAAT
55023 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
55051 GTATGATCTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:55251 original size:13 final size:13
Alignment explanation
Indices: 55231--55262 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
55221 ATTTAAATTC
55231 TATT-TTTAGGAT
1 TATTATTTAGGAT
55243 TATTATTTAGGAT
1 TATTATTTAGGAT
55256 TATTATT
1 TATTATT
55263 ATGATATTGT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 4 0.21
13 15 0.79
ACGTcount: A:0.28, C:0.00, G:0.12, T:0.59
Consensus pattern (13 bp):
TATTATTTAGGAT
Found at i:61601 original size:22 final size:22
Alignment explanation
Indices: 61555--61597 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
61545 ATAAAATTAT
61555 TAAATATTAAAATAAAATAAAA
1 TAAATATTAAAATAAAATAAAA
* *
61577 TAAATATTTAAA-AAATTAAAA
1 TAAATATTAAAATAAAATAAAA
61598 ATAATATGGA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 8 0.42
22 11 0.58
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (22 bp):
TAAATATTAAAATAAAATAAAA
Found at i:64475 original size:212 final size:212
Alignment explanation
Indices: 64108--64532 Score: 773
Period size: 212 Copynumber: 2.0 Consensus size: 212
64098 TTAGTGAACT
* *
64108 TTCTTCTCCTCTGCCTGTGCTTTTTTTCCCGAAAAAGTTTCCACGTAAAATCTGTGTGTTCTTTC
1 TTCTTCTCCTCTGCCCGTACTTTTTTTCCCGAAAAAGTTTCCACGTAAAATCTGTGTGTTCTTTC
*
64173 TCTTGTTTGTTTTATTTACAATATTTCTTCATTGTCGACATTTAATTTAACAGTATTATAAATTT
66 TCTTGTTTATTTTATTTACAATATTTCTTCATTGTCGACATTTAATTTAACAGTATTATAAATTT
64238 TCAATTTTGATGATCTATACTCTTAGGTTTATATCATCTT-TTGATATTAGCATGAAGCCTAAAC
131 TCAATTTTGATGATCTATACTCTTAGGTTTATATCAT-TTATTGATATTAGCATGAAGCCTAAAC
64302 AACATAACTATATATATA
195 AACATAACTATATATATA
*
64320 TTCTTCTCCTCTGCCCGTACTTTTTTTCTCGAAAAAGTTTCCACGTAAAATCTGTGTGTTCTTTC
1 TTCTTCTCCTCTGCCCGTACTTTTTTTCCCGAAAAAGTTTCCACGTAAAATCTGTGTGTTCTTTC
*
64385 TCTT-TTTCATTTTCTTTACAATATTTCTTCATTGTCGACATTTAATTTAACAGTATTATAAATT
66 TCTTGTTT-ATTTTATTTACAATATTTCTTCATTGTCGACATTTAATTTAACAGTATTATAAATT
64449 TTCAATTTTGATGATCTATACTCTTAGGTTTATATCATTTATTGATATTAGCATGAAGCCTAAAC
130 TTCAATTTTGATGATCTATACTCTTAGGTTTATATCATTTATTGATATTAGCATGAAGCCTAAAC
64514 AACATAACTATATATATA
195 AACATAACTATATATATA
64532 T
1 T
64533 ATCACTCATC
Statistics
Matches: 206, Mismatches: 5, Indels: 4
0.96 0.02 0.02
Matches are distributed among these distances:
211 5 0.02
212 201 0.98
ACGTcount: A:0.27, C:0.17, G:0.10, T:0.46
Consensus pattern (212 bp):
TTCTTCTCCTCTGCCCGTACTTTTTTTCCCGAAAAAGTTTCCACGTAAAATCTGTGTGTTCTTTC
TCTTGTTTATTTTATTTACAATATTTCTTCATTGTCGACATTTAATTTAACAGTATTATAAATTT
TCAATTTTGATGATCTATACTCTTAGGTTTATATCATTTATTGATATTAGCATGAAGCCTAAACA
ACATAACTATATATATA
Found at i:73669 original size:16 final size:16
Alignment explanation
Indices: 73648--73679 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
73638 TAACTAAAGG
73648 AATTGAAGTACACTCA
1 AATTGAAGTACACTCA
*
73664 AATTGAAGTATACTCA
1 AATTGAAGTACACTCA
73680 TAGGGAAACT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.44, C:0.16, G:0.12, T:0.28
Consensus pattern (16 bp):
AATTGAAGTACACTCA
Done.